Publications

Articles downloadable on this page are pre-print versions. Their layout, text, and figures likely do not match the published versions exactly.

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Recently published

  • Rastislav Rabatin, Broňa Brejová, Tomáš Vinař. Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data . In J. Hlaváčová, ed., Information Technologies - Applications and Theory (ITAT), number 1885 in CEUR-WS, pp. 48-54, Martinské hole, Slovakia, 2017.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Mário Lipovský, Tomáš Vinař, Broňa Brejová. Approximate Abundance Histograms and Their Use for Genome Size Estimation. In J. Hlaváčová, ed., Information Technologies - Applications and Theory (ITAT), number 1885 in CEUR-WS, pp. 27-34, Martinské hole, Slovakia, 2017.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Brona Brejova, Hana Lichancova, Filip Brazdovic, Andrea Cillingova, Martina Nebohacova, Lubomir Tomaska, Tomas Vinar, Jozef Nosek. Draft Genome Sequence of an Obligate Psychrophilic Yeast, Candida psychrophila NRRL Y-17665T. Genome Announc, 5(35). 2017.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Broňa Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomáš Vinař. Isometric gene tree reconciliation revisited. Algorithms for Molecular Biology, 12:17. 2017. Early version appeared at WABI 2016.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Vladimír Boža, Broňa Brejová, Tomáš Vinař. DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads. PLoS One, 12(6):e0178751. 2017.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     

Journal Articles

  • Brona Brejova, Hana Lichancova, Filip Brazdovic, Andrea Cillingova, Martina Nebohacova, Lubomir Tomaska, Tomas Vinar, Jozef Nosek. Draft Genome Sequence of an Obligate Psychrophilic Yeast, Candida psychrophila NRRL Y-17665T. Genome Announc, 5(35). 2017.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Broňa Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomáš Vinař. Isometric gene tree reconciliation revisited. Algorithms for Molecular Biology, 12:17. 2017. Early version appeared at WABI 2016.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Vladimír Boža, Broňa Brejová, Tomáš Vinař. DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads. PLoS One, 12(6):e0178751. 2017.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Andrew D. Foote, Nagarjun Vijay, Maria C. Avila-Arcos, Robin W. Baird, John W. Durban, Matteo Fumagalli, Richard A. Gibbs, M. Bradley Hanson, Thorfinn S. Korneliussen, Michael D. Martin, Kelly M. Robertson, Vitor C. Sousa, Filipe G. Vieira, Tomas Vinar, Paul Wade, Kim C. Worley, Laurent Excoffier, Phillip A. Morin, M. Thomas P. Gilbert, Jochen B. W. Wolf. Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. Nature Communications, 7:11693. 2016.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Ladislav Rampasek, Randi M. Jimenez, Andrej Luptak, Tomas Vinar, Brona Brejova. RNA motif search with data-driven element ordering. BMC Bioinformatics, 17(1):216. 2016.
    [ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
     
  • Vladimír Boža, Broňa Brejová, Tomáš Vinař. GAML: genome assembly by maximum likelihood. Algorithms for Molecular Biology, 10:18. 2015. Early version at WABI 2014.
    [ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
     
  • Michal Nánási, Tomáš Vinař, Broňa Brejová. Sequence annotation with HMMs: New problems and their complexity. Information Processing Letters, 115(6):635-639. 2015.
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  • Andrew D. Foote, Yue Liu, Gregg W. C. Thomas, Tomas Vinar, Jessica Alfoldi, Jixin Deng, Shannon Dugan, Cornelis E. {van Elk}, Margaret E. Hunter, Vandita Joshi, Ziad Khan, Christie Kovar, Sandra L. Lee, Kerstin Lindblad-Toh, Annalaura Mancia, Rasmus Nielsen, Xiang Qin, Jiaxin Qu, Brian J. Raney, Nagarjun Vijay, Jochen B. W. Wolf, Matthew W. Hahn, Donna M. Muzny, Kim C. Worley, M. Thomas P. Gilbert, Richard A. Gibbs. Convergent evolution of the genomes of marine mammals. Nature Genetics, 47(3):272-275. 2015.
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  • Marmoset Genome Sequencing and Analysis Consortium. The common marmoset genome provides insight into primate biology and evolution. Nature Genetics, 46(8):850-857. 2014.
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  • Brona Brejova, Martin Kravec, Gad M. Landau, Tomas Vinar. Fast computation of a string duplication history under no-breakpoint-reuse. Philos Trans A Math Phys Eng Sci, 372(2016):20130133. 2014. Early version appeared at SPIRE 2011.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • B. Franz Lang, Michaela Jakubkova, Eva Hegedusova, Rachid Daoud, Lise Forget, Brona Brejova, Tomas Vinar, Peter Kosa, Dominika Fricova, Martina Nebohacova, Peter Griac, Lubomir Tomaska, Gertraud Burger, Jozef Nosek. Massive programmed translational jumping in mitochondria. Proceedings of the National Academy of Sciences of the United States of America, 111(16):5926-5931. 2014.
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  • Jakub Kovac. On the complexity of rearrangement problems under the breakpoint distance. Journal of Computational Biology, 21(1):1-15. 2014.
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  • Michal Nanasi, Tomas Vinar, Brona Brejova. Probabilistic approaches to alignment with tandem repeats. Algorithms for Molecular Biology, 9(1):3. 2014. Early version appeared in WABI 2013.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Eva Hegedusova, Brona Brejova, Lubomir Tomaska, Matthias Sipiczki, Jozef Nosek. Mitochondrial genome of the basidiomycetous yeast Jaminaea angkorensis. Current Genetics, 60(1):49-59. 2014.
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  • R. Alan Harris, Suzette D. Tardif, Tomas Vinar, Derek E. Wildman, Julienne N. Rutherford, Jeffrey Rogers, Kim C. Worley, Kjersti M. Aagaard. Evolutionary genetics and implications of small size and twinning incallitrichine primates. Proceedings of the National Academy of Sciences of the United States of America, 111(4):1467-1472. 2014.
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  • Xin Ma, Joanna L. Kelley, Kirsten Eilertson, Shaila Musharoff, Jeremiah D. Degenhardt, Andre L. Martins, Tomas Vinar, Carolin Kosiol, Adam Siepel, Ryan N. Gutenkunst, Carlos D. Bustamante. Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii). PLoS One, 8(10):e77175. 2013.
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  • Huajun Zheng, Wenbao Zhang, Liang Zhang, Zhuangzhi Zhang, Jun Li, Gang Lu, Yongqiang Zhu, Yuezhu Wang, Yin Huang, Jing Liu, Hui Kang, Jie Chen, Lijun Wang, Aojun Chen, Shuting Yu, Zhengchao Gao, Lei Jin, Wenyi Gu, Zhiqin Wang, Li Zhao, Baoxin Shi, Hao Wen, Renyong Lin, Malcolm K. Jones, Brona Brejova, Tomas Vinar, Guoping Zhao, Donald P. McManus, Zhu Chen, Yan Zhou, Shengyue Wang. The genome of the hydatid tapeworm Echinococcus granulosus. Nature genetics, 2013.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Jakub Kováč. Complexity of the path avoiding forbidden pairs problem revisited. Discrete Applied Mathematics, 161(10-11):1506-1512. 2013.
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  • H. Bradley Shaffer et al.. The western painted turtle genome, a model for the evolution of extremephysiological adaptations in a slowly evolving lineage. Genome Biology, 14(3):R28. 2013.
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  • Katharina Jahn, Chunfang Zheng, Jakub Kovac, David Sankoff. A consolidation algorithm for genomes fractionated after higher order polyploidization. BMC Bioinformatics, 13 Suppl 19:S8. 2012.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Sheng Zhu, You-Zhi Cao, Cong Jiang, Bi-Yue Tan, Zhong Wang, Sisi Feng, Liang Zhang, Xiao-Hua Su, Brona Brejova, Tomas Vinar, Meng Xu, Ming-Xiu Wang, Shou-Gong Zhang, Min-Ren Huang, Rongling Wu, Yan Zhou. Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution. BMC genomics, 13:382. 2012.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Jakub Kovac, Robert Warren, Marilia D. V. Braga, Jens Stoye. Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation. Journal of Computational Biology, 18(9):1231-1231. 2011.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Orangutan Genome Sequencing and Analysis Consortium. Comparative and demographic analysis of orang-utan genomes. Nature, 469(7331):529-533. 2011.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • M. Valach, Z. Farkas, D. Fricova, J. Kovac, B. Brejova, T. Vinar, I. Pfeiffer, J. Kucsera, L. Tomaska, B. F. Lang, J. Nosek. Evolution of linear chromosomes and multipartite genomes in yeast mitochondria. Nucleic Acids Research, 39(10):4202-4219. 2011.
    [ Abstract ] [ Preprint, 15365Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
     
  • Giltae Song, Luoxin Zhang, Tomas Vinar, Webb Miller. CAGE: Combinatorial Analysis of Gene-Cluster Evolution. Journal of Computational Biology, 17(9):1227-1232. 2010. Early version appeared in RECOMB-CG 2009.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Tomas Vinar, Brona Brejova, Giltae Song, Adam C. Siepel. Reconstructing Histories of Complex Gene Clusters on a Phylogeny. Journal of Computational Biology, 17(9):1267-1279. 2010. Early version appeared in RECOMB-CG 2009.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Matej Vesteg, Rostislav Vacula, Jurgen M. Steiner, Bianka Mateasikova, Wolfgang Loffelhardt, Brona Brejova, Juraj Krajcovic. A possible role for short introns in the acquisition of stroma-targeting peptides in the flagellate Euglena gracilis. DNA Research, 17(4):223-231. 2010.
    [ Abstract ] [ Preprint, 191Kb ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Rute R. {da Fonseca}, Carolin Kosiol, Tomas Vinar, Adam Siepel, Rasmus Nielsen. Positive selection on apoptosis related genes. FEBS letters, 584(3):469-476. 2010.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Panda Genome Sequencing and Analysis Consortium. The sequence and de novo assembly of the giant panda genome. Nature, 463(7279):269-392. 2010.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • The MGC Project Team. The completion of the Mammalian Gene Collection (MGC). Genome research, 19(12):2324-2333. 2009.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Yu Zhang, Giltae Song, Tomas Vinar, Eric D. Green, Adam Siepel, Webb Miller. Evolutionary History Reconstruction for Mammalian Complex Gene Clusters. Journal of Computational Biology, 16(8):1051-1070. 2009. Early version appeared in RECOMB 2008.
    [ Abstract ] [ Preprint, 965Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium . The Schistosoma japonicum genome reveals features of host-parasite interplay. Nature, 460(7253):345-351. 2009.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Brona Brejova, Tomas Vinar, Yangyi Chen, Shengyue Wang, Guoping Zhao, Daniel G. Brown, Ming Li, Yan Zhou. Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence. Nucleic Acids Research, 37(7):e52. 2009.
    [ Abstract ] [ Preprint, 153Kb ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Avril Coghlan, Tristan J. Fiedler, Sheldon J. McKay, Paul Flicek, Todd W. Harris, Darin Blasiar, {The nGASP Consortium}, Lincoln D. Stein. nGASP - the nematode genome annotation assessment project . BMC Bioinformatics, 9:549. 2008.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Carolin Kosiol, Tomas Vinar, Rute R. {da Fonseca}, Melissa J. Hubisz, Carlos D. Bustamante, Rasmus Nielsen, Adam Siepel. Patterns of positive selection in six Mammalian genomes. PLoS Genetics, 4(8):e1000144. 2008.
    [ Abstract ] [ Preprint, 538Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
     
  • Adam Siepel, Mark Diekhans, Brona Brejova, Laura Langton, Michael Stevens, Charles L. G. Comstock, Colleen Davis, Brent Ewing, Shelly Oommen, Christopher Lau, Hung-Chun Yu, Jianfeng Li, Bruce A. Roe, Phil Green, Daniela S. Gerhard, Gary Temple, David Haussler, Michael R. Brent. Targeted discovery of novel human exons by comparative genomics. Genome research, 17(12):1763-1763. 2007.
    [ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
     
  • Xuefeng Cui, Tomas Vinar, Brona Brejova, Dennis Shasha, Ming Li. Homology Search for Genes. Bioinformatics, 23(13):i97-i103. 2007. Intelligent Systems for Molecular Biology (ISMB 2007).
    [ Abstract ] [ Preprint, 159Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
     
  • Rhesus Macaque Genome Sequencing and Analysis Consortium. Evolutionary and biomedical insights from the rhesus macaque genome. Science, 316(5822):222-234. April 2007.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Brona Brejova, Daniel G. Brown, Tomas Vinar. The most probable labeling problem in HMMs and its application to bioinformatics. Journal of Computer and System Sciences, 73(7):1060-1077. 2007. Early version in WABI 2004.
    [ Abstract ] [ Preprint, 335Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Brona Brejova, Daniel G. Brown, Ming Li, Tomas Vinar. ExonHunter: A Comprehensive Approach to Gene Finding. Bioinformatics, 21(S1):i57-i65. 2005. Intelligent Systems for Molecular Biology (ISMB 2005).
    [ Abstract ] [ Preprint, 144Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
     
  • Brona Brejova, Daniel G. Brown, Tomas Vinar. Vector seeds: an extension to spaced seeds. Journal of Computer and System Sciences, 70(3):364-380. May 2005. Special issue on bioinformatics. Early version in WABI 2003.
    [ Abstract ] [ Preprint, 406Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Brona Brejova, Daniel G. Brown, Tomas Vinar. Optimal Spaced Seeds for Homologous Coding Regions. Journal of Bioinformatics and Computational Biology, 1(4):595-610. January 2004. Early version appeared in CPM 2003.
    [ Abstract ] [ Preprint, 2657Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
     
  • Therese Biedl, Brona Brejova, Erik D. Demaine, Angele M. Hamel, Alejandro Lopez-Ortiz, Tomas Vinar. Finding Hidden Independent Sets in Interval Graphs. Theoretical Computer Science, 310(1-3):287-307. January 2004. Early version appeared in COCOON 2003.
    [ Abstract ] [ Preprint, 216Kb ] [ Download from publisher ] [ BibTeX ] [ MathSciNet ]
     

Conference Articles (not published elsewhere)

  • Rastislav Rabatin, Broňa Brejová, Tomáš Vinař. Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data . In J. Hlaváčová, ed., Information Technologies - Applications and Theory (ITAT), number 1885 in CEUR-WS, pp. 48-54, Martinské hole, Slovakia, 2017.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Mário Lipovský, Tomáš Vinař, Broňa Brejová. Approximate Abundance Histograms and Their Use for Genome Size Estimation. In J. Hlaváčová, ed., Information Technologies - Applications and Theory (ITAT), number 1885 in CEUR-WS, pp. 27-34, Martinské hole, Slovakia, 2017.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Martin Macko, Martin Králik, Broňa Brejová, Tomáš Vinař. OB-Fold Recognition Combining Sequence and Structural Motifs. In B. Brejová, ed., Information Technologies - Applications and Theory (ITAT), number 1649 in CEUR-WS, pp. 18-25, Tatranské Matliare, Slovakia, 2016.
    [ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
     
  • Vladimír Boža, Jakub Jursa, Tomáš Vinař, Broňa Brejová. Fishing in Read Collections: Memory Efficient Indexing for Sequence Assembly. In Costas S. Iliopoulos, Simon J. Puglisi, Emine Yilmaz, ed., String Processing and Information Retrieval (SPIRE), 9309 volume of Lecture Notes in Computer Science, pp. 188-198, London, UK, September 2015. Springer.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Michal Hozza, Tomáš Vinař, Broňa Brejová. How Big is That Genome? Estimating Genome Size and Coverage from k-mer Abundance Spectra. In Costas S. Iliopoulos, Simon J. Puglisi, Emine Yilmaz, ed., String Processing and Information Retrieval (SPIRE), 9309 volume of Lecture Notes in Computer Science, pp. 199-209, London, UK, September 2015. Springer.
    [ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
     
  • Andrej Ridzik, Broňa Brejová. Neuropeptide Recognition by Machine Learning Methods. In V. Kurkova, L. Bajer, V. Svatek, ed., Information Technologies - Applications and Theory (ITAT), number 1003 in CEUR-WS, pp. 72-78, Jasna, Slovakia, 2014.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Albert Herencsár, Broňa Brejová . An Improved Algorithm for Ancestral Gene Order Reconstruction. In V. Kurkova, L. Bajer, V. Svatek, ed., Information Technologies - Applications and Theory (ITAT), number 1003 in CEUR-WS, pp. 46-53, Jasna, Slovakia, 2014.
    [ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
     
  • Martina Višňovská, Tomáš Vinař, Broňa Brejová. DNA Sequence Segmentation Based on Local Similarity. In Tomáš Vinař, ed., Information Technologies - Applications and Theory (ITAT), 1003 volume of CEUR-WS, pp. 36-43, 2013.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Martin Kravec, Martin Bobák, Broňa Brejová, Tomáš Vinař. Variants of Genes from the Next Generation Sequencing Data. In Tomáš Vinař, ed., Information Technologies - Applications and Theory (ITAT), 1003 volume of CEUR-WS, pp. 44-51, 2013.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Peter Kovac, Brona Brejova, Tomas Vinar. Aligning Sequences with Repetitive Motifs. In Information Technologies - Applications and Theory (ITAT), pp. 41-48, 2012. Best paper award.
    [ Abstract ] [ Preprint, 618Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Marcel Kucharik, Jakub Kovac, Brona Brejova. Gene finding with complex external information. In Markéta Lopatková, ed., Information Technologies - Applications and Theory (ITAT), 788 volume of CEUR-WS, pp. 39-46, Vrátna dolina, Slovakia, September 2011. Best paper award.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Brona Brejova, Michal Burger, Tomas Vinar. Automated Segmentation of DNA Sequences with Complex Evolutionary Histories. In Teresa M. Przytycka, Marie-France Sagot, ed., Algorithms in Bioinformatics, 11th International Workshop (WABI), 6833 volume of Lecture Notes in Computer Science, pp. 1-13, Saarbrücken, Germany, September 2011. Springer.
    [ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
     
  • Jakub Kovac, Brona Brejova, Tomas Vinar. A Practical Algorithm for Ancestral Rearrangement Reconstruction. In Teresa M. Przytycka, Marie-France Sagot, ed., Algorithms in Bioinformatics, 11th International Workshop (WABI), 6833 volume of Lecture Notes in Computer Science, pp. 163-174, Saarbrücken, Germany, September 2011. Springer.
    [ Abstract ] [ Preprint, 450Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
     
  • Martina Visnovska, Michal Nanasi, Tomas Vinar, Brona Brejova. Estimating effective DNA database size via compression. In Information Technologies, Applications and Theory (ITAT), 683 volume of CEUR-WS, pp. 63-70, Smrekovica, Slovakia, 2010. Best paper award.
    [ Abstract ] [ Preprint, 109Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Michal Nanasi, Tomas Vinar, Brona Brejova. The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection. In A. Amir and L. Parida, ed., Combinatorial Pattern Matching, 21th Annual Symposium (CPM 2010), 6129 volume of Lecture Notes in Computer Science, pp. 164-176, Brooklyn, New York, USA, 2010. Springer.
    [ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
     
  • Jakub Kovac, Tomas Vinar, Brona Brejova. Predicting Gene Structures from Multiple RT-PCR Tests. In Steven L. Salzberg, Tandy Warnow, ed., Algorithm in Bioinformatics, 9th International Workshop (WABI), 5724 volume of Lecture Notes in Bioinformatics, pp. 181-193, Philadelphia, PA, September 2009. Springer.
    [ Abstract ] [ Preprint, 325Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Rastislav Sramek, Brona Brejova, Tomas Vinar. On-line Viterbi Algorithm for Analysis of Long Biological Sequences. In Raffaele Giancarlo, Sridhar Hannenhalli, ed., Algorithms in Bioinformatics: 7th International Workshop (WABI), 4645 volume of Lecture Notes in Computer Science, pp. 240-251, Philadelphia, PA, USA, September 2007. Springer.
    [ Abstract ] [ Preprint, 243Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Brona Brejova, Daniel G. Brown, Ian M. Harrower, Tomas Vinar. New bounds for motif finding in strong instances. In Combinatorial Pattern Matching, 17th Annual Symposium (CPM 2006), 4009 volume of Lecture Notes in Computer Science, pp. 94-105, Barcelona, Spain, July 2006.
    [ Abstract ] [ Preprint, 410Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Brona Brejova, Daniel G. Brown, Ian M. Harrower, Alejandro Lopez-Ortiz, Tomas Vinar. Sharper Upper and Lower Bounds for an Approximation Scheme for CONSENSUS-PATTERN. In Alberto Apostolico, Maxime Crochemore, Kunsoo Park, ed., Combinatorial Pattern Matching, 16th Annual Symposium (CPM), 3537 volume of Lecture Notes in Computer Science, pp. 1-10, Jeju Island, Korea, June 19-22 2005. Springer.
    [ Abstract ] [ Preprint, 143Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Brona Brejova, Daniel G. Brown, Tomas Vinar . Optimal DNA signal recognition models with a fixed amount of intrasignal dependency. In G. Benson, R. Page, ed., Algorithms and Bioinformatics: 3rd International Workshop (WABI), 2812 volume of Lecture Notes in Bioinformatics, pp. 78-94, Budapest, Hungary, September 2003. Springer.
    [ Abstract ] [ Preprint, 111Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Brona Brejova, Tomas Vinar. A Better Method for Length Distribution Modeling in HMMs and Its Application to Gene Finding . In A. Apostolico, M. Takeda, ed., Combinatorial Pattern Matching, 13th Annual Symposium (CPM), 2373 volume of Lecture Notes in Computer Science, pp. 190-202, Fukuoka, Japan, July 3-5 2002. Springer.
    [ Abstract ] [ Preprint, 209Kb ] [ Download from publisher ] [ BibTeX ] [ MathSciNet ]
     

Books and Book Chapters

  • Jozef Nosek, Brona Brejova, Martina Nebohacova, Peter Barath, Ingrid Bhatia-Kissova, Ivan Valent, Richard Kollar, Lubomir Tomaska. Genomika. 2013. CreateSpace. Textbook in Slovak language.
    [ Abstract ] [ Webpage ] [ BibTeX ]
     
  • Randi M. Jimenez, Ladislav Rampášek, Broňa Brejová, Tomáš Vinař, Andrej Lupták. Discovery of RNA Motifs Using a Computational Pipeline that Allows Insertions in Paired Regions and Filtering of Candidate Sequences . In Jörg S. Hartig, ed., Ribozymes: Methods and Protocols, 848 volume of Methods in Molecular Biology, chapter 10, pp. 145-158, 2012. Springer.
    [ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
     
  • Brona Brejova, Daniel G. Brown, Tomas Vinar. Advances in hidden Markov models for sequence annotation. In I. I. Mandoiu, A. Zelikovski, ed., Bioinformatics Algorithms: Techniques and Applications, chapter 4, pp. 55-92, 2008. Wiley.
    [ Abstract ] [ Preprint, 369Kb ] [ BibTeX ]
     
  • Brona Brejova, Tomas Vinar, Ming Li. Pattern Discovery: Methods and Software. In Stephen A. Krawetz, David D. Womble, ed., Introduction to Bioinformatics, chapter 29, pp. 491-522, 2003. Humana Press.
    [ Abstract ] [ Preprint, 365Kb ] [ BibTeX ]
     

Theses

  • Vladimír Boža. Algorithms for high-throughput sequencing data. PhD thesis, Comenius University in Bratislava, 2017. Supervised by Tomáš Vinař.
    [ Abstract ] [ BibTeX ]
     
  • Mário Lipovský. Approximate Abundance Histograms and Their Use for Genome Size Estimation. Bachelor thesis, Comenius University in Bratislava, 2017. Supervised by Broňa Brejová.
    [ Abstract ] [ BibTeX ]
     
  • Radoslav Chládek. Vizualizácia evolučných histórií genómov s viacerými chromozómami. Bachelor thesis, Comenius University in Bratislava, 2017. Supervised by Broňa Brejová.
    [ Abstract ] [ BibTeX ]
     
  • Matúš Zeleňák. Sampling from MinION Reads. Bachelor thesis, Comenius University in Bratislava, 2017. Supervised by Tomáš Vinař.
    [ Abstract ] [ BibTeX ]
     
  • Jakub Havelka. Alignment of Nanopore Sequencing Squiggles. Bachelor thesis, Comenius University in Bratislava, 2017. Supervised by Tomáš Vinař.
    [ Abstract ] [ BibTeX ]
     
  • Marcel Schichman. Oprava chýb v dlhých čítaniach bez použitia zarovnávania. Master thesis, Comenius University in Bratislava, 2017. Supervisor Vladimír Boža, Tomáš Vinař.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Peter Koza. Grafické prostredie na zobrazovanie a editovanie RNA motívov. Bachelor thesis, Comenius University in Bratislava, 2016. Supervised by Broňa Brejová.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Dávid Simeunovič. Vizualizácia evolučných histórií. Bachelor thesis, Comenius University in Bratislava, 2016. Supervised by Broňa Brejová.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Rastislav Rabatin. Alignment of Nanopore Sequencing Reads. Bachelor thesis, Comenius University in Bratislava, 2016. Supervised by Tomáš Vinař.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Jaroslav Petrucha. Efektívna reprezentácia množiny krátkych reťazcov. Bachelor thesis, Comenius University in Bratislava, 2016. Supervised by Tomáš Vinař.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Peter Kuljovský. Efektívne vyhľadávanie krátkych reťazcov v dlhej sekvencii. Bachelor thesis, Comenius University in Bratislava, 2016. Supervised by Vlado Boža.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Ján Hozza. Rekonštrukcia histórií génových zhlukov. Master thesis, Comenius University in Bratislava, 2016. Supervised by Tomáš Vinař.
    [ Abstract ] [ BibTeX ]
     
  • Marcel Schichman. Zarovnávanie sekvenovacích dát s vysokým počtom chýb. Bachelor thesis, Comenius University in Bratislava, 2015. Supervised by Vladimír Boža.
    [ Abstract ] [ BibTeX ]
     
  • Jakub Jursa. Dátové štruktúry pre uchovávanie sekvenovacích dát. Master thesis, Comenius University in Bratislava, 2015. Supervised by Vlado Boža.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Ján Hozza. Rekonštrukcia duplikačných histórií pomocou pravdepodobnostného modelu. Bachelor thesis, Comenius University in Bratislava, 2014. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 499Kb ] [ BibTeX ]
     
  • Michal Anderle. Časovanie udalostí pri inferencii duplikačných histórií. Bachelor thesis, Comenius University in Bratislava, 2014. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 826Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Petra Kubincová. Mapping between Genomes. Bachelor thesis, Comenius University in Bratislava, 2014. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 993Kb ] [ BibTeX ]
     
  • Veronika Ženišová. Algoritmy na rekonštrukciu genómov pomocou preusporiadania. Master thesis, Comenius University in Bratislava, 2014. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 1785Kb ] [ BibTeX ]
     
  • Lukáš Bača. Trénovanie parametrov pre hľadanie génov s využitím externej informácie. Master thesis, Comenius University in Bratislava, 2014. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 2354Kb ] [ BibTeX ]
     
  • Albert Herencsár. An improved algorithm for ancestral gene order reconstruction. Master thesis, Comenius University in Bratislava, 2014. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 984Kb ] [ BibTeX ]
     
  • Soňa Gibaštíková. Finding Conserved Gene Clusters in Duplicated Genomes. Master thesis, Comenius University in Bratislava, 2014. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 1410Kb ] [ BibTeX ]
     
  • Andrej Ridzik. Algoritmy na rozpoznávanie neuropeptidov. Master thesis, Comenius University in Bratislava, 2014. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 815Kb ] [ BibTeX ]
     
  • Michal Hozza. Zarovnávanie sekvencií s použitím metód klasifikácie. Master thesis, Comenius University in Bratislava, 2014. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 890Kb ] [ BibTeX ]
     
  • Pavol Kmeč. Vykresľovanie RNA motívov. Master thesis, Comenius University in Bratislava, 2013. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 6937Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Martina Višňovská. Alignments on Sequences with Internal Structure. PhD thesis, Comenius University in Bratislava, 2013. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 1733Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Jakub Kováč. Algorithms for Genome Rearrangements. PhD thesis, Comenius University in Bratislava, 2013. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 2874Kb ] [ BibTeX ]
     
  • Martin Bobák. Identifikácia variantov génov z dát sekvenovania novej generácie. Master thesis, Comenius University in Bratislava, 2013. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 1006Kb ] [ BibTeX ]
     
  • Martin Višňovec. Systém na hľadanie ortológov v príbuzných genómoch . Master thesis, Comenius University in Bratislava, 2013. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 960Kb ] [ BibTeX ]
     
  • Martin Macko. Algoritmus pre hľadanie vzdialených funkčných ortológov a jeho aplikácia na OB-fold doménu. PhD thesis, Comenius University in Bratislava, 2013. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 1248Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Michal Petrucha. Data Structures for Whole-Genome Alignments . Bachelor thesis, Comenius University in Bratislava, 2012. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 481Kb ] [ BibTeX ]
     
  • Jakub Kováč (ml). Kompresia genómu za pomoci skrytých Markovovských modelov. Bachelor thesis, Comenius University in Bratislava, 2012. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 499Kb ] [ BibTeX ]
     
  • Ladislav Rampášek. Computational Complexity and Practical Implementation of RNA Motif Search. Master thesis, Comenius University in Bratislava, 2012. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 1575Kb ] [ BibTeX ]
     
  • Peter Kováč. Bioinformatics of Sequences with Repetitive Motifs. Master thesis, Comenius University in Bratislava, 2012. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 1389Kb ] [ BibTeX ]
     
  • Milan Mikula. Anotácia zhlukov génov. Bachelor thesis, Comenius University in Bratislava, 2011. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 2650Kb ] [ BibTeX ]
     
  • Andrej Ridzik. Použitie komparatívnej informácie pri hľadaní génov. Bachelor thesis, Comenius University in Bratislava, 2011. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 1064Kb ] [ BibTeX ]
     
  • Jaroslav Budiš. Discovering motifs in mitochondrial DNA. Master thesis, Comenius University in Bratislava, 2011. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 4096Kb ] [ BibTeX ]
     
  • Martin Kravec. MCMC algoritmus na rekonštrukciu duplikačných histórií. Master thesis, Comenius University in Bratislava, 2011. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 1364Kb ] [ BibTeX ]
     
  • Martin Králik. Pravdepodobnostné modely pre alternatívny zostrih génov. Master thesis, Comenius University in Bratislava, 2011. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 957Kb ] [ BibTeX ]
     
  • Marcel Kucharík. A New Algorithm for Using External Information in Gene Finding. Master thesis, Comenius University in Bratislava, 2011. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 989Kb ] [ BibTeX ]
     
  • Peter Herman. Grafické prostredie na editovanie RNA motívov. Bachelor thesis, Comenius University in Bratislava, 2010. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 503Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
     
  • Peter Kováč. Implementácia externých zdrojov dát v hľadaní génov. Bachelor thesis, Comenius University in Bratislava, 2010. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 1558Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
     
  • Ladislav Rampášek. RNA motif search in genomic sequences. Bachelor thesis, Comenius University in Bratislava, 2010. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 821Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
     
  • Juraj Mešťánek. Software for Annotation of Protein Coding Genes in Yeast Mitochondrial Genomes. Master thesis, Comenius University in Bratislava, 2010. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 800Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
     
  • Michal Burger. Atomization of DNA Sequences with Complex Evolutionary History. Master thesis, Comenius University in Bratislava, 2010. Supervised by Tomáš Vinař.
    [ Abstract ] [ Preprint, 800Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Michal Nánási. Biological sequence annotation with hidden Markov models. Master thesis, Comenius University in Bratislava, 2010. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 739Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
     
  • Jakub Kováč. Gene Finding Using RT-PCR Tests. Master thesis, Comenius University in Bratislava, 2009. Supervised by Broňa Brejová.
    [ Abstract ] [ Preprint, 843Kb ] [ Download from publisher ] [ BibTeX ]
     
  • Rastislav Šrámek. The On-line Viterbi Algorithm. Master thesis, Comenius University in Bratislava, 2007. Supervised by Tomáš Vinař and Broňa Brejová.
    [ Abstract ] [ Preprint, 616Kb ] [ Download from publisher ] [ BibTeX ]
     

Technical Reports

  • Vladimír Boža, Broňa Brejová, Tomáš Vinař. Improving Nanopore Reads Raw Signal Alignment. Technical Report arXiv:1705.01620, arXiv, 2017.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Rastislav Rabatin, Broňa Brejová, Tomáš Vinař. Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data. Technical Report arXiv:1606.08719, arXiv, 2016.
    [ Abstract ] [ Download from publisher ] [ BibTeX ]
     
  • Therese Biedl, Brona Brejova, Erik D. Demaine, Angele M. Hamel, Tomas Vinar. Optimal Arrangement of Leaves in the Tree Representing Hierarchical Clustering of Gene Expression Data. Technical Report CS-2001-14, University of Waterloo, April 2001.
    [ Abstract ] [ Preprint, 556Kb ] [ Webpage ] [ BibTeX ]